[phenixbb] Phenix.refine coordinate error estimate discrepancies
Phil Jeffrey
pjeffrey at Princeton.EDU
Tue Jul 21 12:44:00 PDT 2009
There seems to be a large discrepancy between the likelihood-based
coordinate error estimate depending on whether the intensities or
structure factor magnitudes are used, which doesn't make any sense to me.
If I do:
% phenix.refine rebuild.pdb data_withI.mtz
phenix.refine picks up Imean and SigImean from the MTZ and refines the
structure
xray_data {
file_name = "data_withI.mtz"
labels = "IMEAN,SIGIMEAN"
r_free_flags {
file_name = "data_withI.mtz"
label = "FreeR_flag"
test_flag_value = 0
}
then I get:
| maximum likelihood estimate for coordinate error: 1.39 A
But if I create an MTZ file without the intensities by using CAD on the
original file, and use the same coordinate file:
% phenix.refine rebuild.pdb data_withoutI.mtz
phenix.refine picks up the structure factors instead:
xray_data {
file_name = "data_withoutI.mtz"
labels = "F,SIGF"
r_free_flags {
file_name = "data_withoutI.mtz"
label = "FreeR_flag"
test_flag_value = 0
}
}
then this seems to be the right ballpark for a 1.75 Angstrom structure....
| maximum likelihood estimate for coordinate error: 0.28 A
Similar R-factors, but there is a factor of 10 difference in the scale
reported here:
I's:
r_work= 0.2266 r_free= 0.2570 ksol= 0.41 Bsol= 50.00 scale= 0.097
F's:
r_work= 0.2221 r_free= 0.2557 ksol= 0.41 Bsol= 50.00 scale= 0.965
Version: 1.4
Release tag: 3
cctbx tag: 2008_12_07_1353
Platform: mac-intel-osx osx-10.5.6
User: phil
Cheers,
Phil Jeffrey
Princeton
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